Had the same issue (mods not showing up in Launcher), and stumbled over this thread, which did point me into the right direction to look.
Everything worked until a mod had an update today. After a while checking this and that, I noticed that I still had the old key in my keys folder, plus the new one. Since I use symlinks (Linux Server), the old key did point into nothing. Removed that broken link, and everything shows up again in the Launcher.
Might me interesting for the next guy who's getting grey hair because of that ;)
Hanky